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2018-bioinfosummer-scrnaseq

acorde

Isoform co-usage networks from single-cell RNA-seq data

alra

Imputation method for scRNA-seq based on low-rank approximation

amp_phase1_ra

Accelerating Medicines Partnership: Rheumatoid Arthritis Phase 1

asap_o_matic

CL python script to reformat CITEATAC fastqs for kite (kallisto | bustools) processing

autoimpute

An autoencoder based imputation of the sparse single cell RNA-seq data.

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

azimuth

Fork of Azimuth (Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency), updated to work with Python 3.10+

baseline

Reproducible workflows for the data analysis of "Baseline" project

beginning_r

Resources to learn how to use and program in R

betterposter

👩‍🔬👨‍🔬 Another R Markdown Better Scientific Poster

bgg

various projects with data from boardgamegeek

boardgamegeek

A Python interface to boardgamegeek.com. Pulls information from BGG and creates Python objects for the data.

cassini

ELEGOO 3D printer network protocol client

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

cellranger-scripts

Generate samplesheets, config files, and job manager scripts for processing 10X Genomics single cell data with Cell Ranger

cellranger_job_templates

Quickly generate SLURM job scripts for Cellranger functions. NOTE: this has been retired in favor of cellranger-scripts

cellrangerrkit

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere)

celltypist

A tool for semi-automatic cell type classification

cite-seq-count

A tool that allows to get UMI counts from a single cell protein assay

clusterfractions

clustering

CLI to apply UMAP/Leiden clustering to an array of values

cna

Multi-condition single-cell

computational_lab_manual

We wrote a getting-started file for reproducible research in computational science (computational biology).

configs

Config files used to define parameters specific to compute environments at different Institutions

control

RStudio and/or Jupyterlab-focused Docker containers for transcriptomics work

cookiecutter-data-science

Project structure for data project

cookiecutter-wordpress

cytobank-uploader

A command line interface to upload FCS files to Cytobank

dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data